If you don't use our version of the GA tracking code on your site, you would not be engaging our built-in GA support at all, so in that case you'd be welcome to use Universal Analytics tracking code in your site and thank-you pages instead. I gather there's no way to revert to legacy GA once you enable UA, so take that into consideration.
Bear in mind this would give up your ability to track cart button clicks and use Ecommerce Tracking, which is really only possible in our thank-you pages when we're generating the Ecommerce Tracking code from our end.